RNA Velocity using VelocityObject.py object¶

Data : CITEseq from OWHA atlas

Author: Marissa Esteban

In [2]:
# Setup
import scanpy as sc
import scvelo as scv
import anndata
import loompy
import mygene
import scipy
import seaborn as sns
import matplotlib.pyplot as plt
from VelocityObject import VelocityObject
import pandas as pd
In [2]:
# Creating object for IntegratedMultimodal_CITEseq with ALL TIME POINTS

h5ad_path = "/Volumes/PortableSSD/SRSP/IntegratedMultimodal_CITEseq.h5ad"
loom_paths = ["/Volumes/PortableSSD/SRSP/YS001/possorted_genome_bam_KLWV0.loom",
              "/Volumes/PortableSSD/SRSP/YS002/possorted_genome_bam_PNEM4.loom",
              "/Volumes/PortableSSD/SRSP/YS003/possorted_genome_bam_8Q2XV.loom",
              "/Volumes/PortableSSD/SRSP/YS004/possorted_genome_bam_0XB2N.loom",
              "/Volumes/PortableSSD/SRSP/YS005/possorted_genome_bam_HX08G.loom",
              "/Volumes/PortableSSD/SRSP/YS006/possorted_genome_bam_751VB.loom"]

citeSEQ_all = VelocityObject(h5ad_path, loom_paths)

WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:biothings.client:Input sequence provided is already in string format. No operation performed
WARNING:biothings.client:Input sequence provided is already in string format. No operation performed
INFO:biothings.client:querying 1-248 ...

==== Converting ENSEMBL Genes ====
Total ldata genes: 33696
ENSEMBL-like genes: 248
Already-symbol-like genes: 33448 


INFO:biothings.client:Finished.
WARNING:biothings.client:13 input query terms found no hit:	['ENSMUSG00000095742', 'ENSMUSG00000095728', 'ENSMUSG00000095076', 'ENSMUSG00000121317', 'ENSMUSG000
INFO:biothings.client:Pass "returnall=True" to return complete lists of duplicate or missing query terms.

Mapped ENSMUSG → symbol: 203
Unmapped ENSMUSG: 45
Total ENSMUSG IDs after mapping:  45

=== Removing duplicates ===
adata
Cells (original): 35317
Genes (original): 30481
Duplicate cell barcodes: 144
Duplicate genes: 0
ldata
Cells (original): 45487
Genes (original): 33696
Duplicate cell barcodes: 235
Duplicate genes: 27

 adata after dedup: (35173, 30481)
ldata after dedup: (45252, 33696)

=== Subsetting cells by GENES and BARCODES ===
Overlapping Cells: 34946
Overlapping genes: 29365

adata shape: (34946, 29365)
ldata shape: (34946, 29365)
Cells match: True
Genes match: True

Layers in adata_subset: ['spliced', 'unspliced', 'ambiguous']
Spliced shape: (34946, 29365)
Unspliced shape: (34946, 29365)

=== Seurat-derived AnnData (adata) ===
Cells (obs): 34946
Genes (var): 29365
First 10 cell names: ['AAACCCAAGAACAGGA', 'AAACCCAAGATACAGT', 'AAACCCAAGCAATAGT', 'AAACCCAAGCGCCTAC', 'AAACCCAAGCTAGTTC', 'AAACCCAAGGTACCTT', 'AAACCCAAGTATCTGC', 'AAACCCAAGTCTCTGA', 'AAACCCACAACCCTAA', 'AAACCCACAAGAAATC']
First 10 gene names: ['Xkr4', 'Gm19938', 'Sox17', 'Mrpl15', 'Lypla1', 'Tcea1', 'Rgs20', 'Atp6v1h', 'Npbwr1', '4732440D04Rik']

=== Loom Spliced/Unspliced Data (ldata) ===
Cells (obs): 34946
Genes (var): 29365
First 10 cell names: ['AAACCCAAGAACAGGA', 'AAACCCAAGATACAGT', 'AAACCCAAGCAATAGT', 'AAACCCAAGCGCCTAC', 'AAACCCAAGCTAGTTC', 'AAACCCAAGGTACCTT', 'AAACCCAAGTATCTGC', 'AAACCCAAGTCTCTGA', 'AAACCCACAACCCTAA', 'AAACCCACAAGAAATC']
First 10 gene names: ['Xkr4', 'Gm19938', 'Sox17', 'Mrpl15', 'Lypla1', 'Tcea1', 'Rgs20', 'Atp6v1h', 'Npbwr1', '4732440D04Rik']

Layer Shapes in ldata
spliced: (34946, 29365)
unspliced: (34946, 29365)
ambiguous: (34946, 29365)
VelocityObject initialized successfully.
In [17]:
h5ad_path_keratinocytes_all = "/Volumes/PortableSSD/SRSP/KeratinocytesAnnotated_CITEseq.h5ad"
h5ad_path_keratinocytes_uw = "/Volumes/PortableSSD/SRSP/Keratinocytes_UW.h5ad"
h5ad_path_keratinocytes_wo = "/Volumes/PortableSSD/SRSP/Keratinocytes_WO.h5ad"

loom_paths = ["/Volumes/PortableSSD/SRSP/YS001/possorted_genome_bam_KLWV0.loom",
              "/Volumes/PortableSSD/SRSP/YS002/possorted_genome_bam_PNEM4.loom",
              "/Volumes/PortableSSD/SRSP/YS003/possorted_genome_bam_8Q2XV.loom",
              "/Volumes/PortableSSD/SRSP/YS004/possorted_genome_bam_0XB2N.loom",
              "/Volumes/PortableSSD/SRSP/YS005/possorted_genome_bam_HX08G.loom",
              "/Volumes/PortableSSD/SRSP/YS006/possorted_genome_bam_751VB.loom"]

#citeSEQ_keratinocytes = VelocityObject(h5ad_path_keratinocytes_all, loom_paths)
citeSEQ_keratinocytes_uw = VelocityObject(h5ad_path_keratinocytes_uw, loom_paths)
#citeSEQ_keratinocytes_wo = VelocityObject(h5ad_path_keratinocytes_wo, loom_paths)

WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:biothings.client:Input sequence provided is already in string format. No operation performed
WARNING:biothings.client:Input sequence provided is already in string format. No operation performed
INFO:biothings.client:querying 1-248 ...

==== Converting ENSEMBL Genes ====
Total ldata genes: 33696
ENSEMBL-like genes: 248
Already-symbol-like genes: 33448 


INFO:biothings.client:Finished.
WARNING:biothings.client:13 input query terms found no hit:	['ENSMUSG00000095742', 'ENSMUSG00000095728', 'ENSMUSG00000095076', 'ENSMUSG00000121317', 'ENSMUSG000
INFO:biothings.client:Pass "returnall=True" to return complete lists of duplicate or missing query terms.

Mapped ENSMUSG → symbol: 203
Unmapped ENSMUSG: 45
Total ENSMUSG IDs after mapping:  45

=== Removing duplicates ===
adata
Cells (original): 6317
Genes (original): 30481
Duplicate cell barcodes: 0
Duplicate genes: 0
ldata
Cells (original): 45487
Genes (original): 33696
Duplicate cell barcodes: 235
Duplicate genes: 27

 adata after dedup: (6317, 30481)
ldata after dedup: (45252, 33696)

=== Subsetting cells by GENES and BARCODES ===
Overlapping Cells: 6224
Overlapping genes: 29365

adata shape: (6224, 29365)
ldata shape: (6224, 29365)
Cells match: True
Genes match: True

Layers in adata_subset: ['spliced', 'unspliced', 'ambiguous']
Spliced shape: (6224, 29365)
Unspliced shape: (6224, 29365)

=== Seurat-derived AnnData (adata) ===
Cells (obs): 6224
Genes (var): 29365
First 10 cell names: ['AAACCCAAGGTACCTT', 'AAACCCAAGTCTCTGA', 'AAACGAAAGATTCGCT', 'AAACGAAAGCTCACTA', 'AAACGAAGTACTGACT', 'AAACGAAGTGTATCCA', 'AAACGAAGTTGCTCGG', 'AAACGAATCATTTGGG', 'AAACGAATCCGTATGA', 'AAACGAATCTCAACCC']
First 10 gene names: ['Xkr4', 'Gm19938', 'Sox17', 'Mrpl15', 'Lypla1', 'Tcea1', 'Rgs20', 'Atp6v1h', 'Npbwr1', '4732440D04Rik']

=== Loom Spliced/Unspliced Data (ldata) ===
Cells (obs): 6224
Genes (var): 29365
First 10 cell names: ['AAACCCAAGGTACCTT', 'AAACCCAAGTCTCTGA', 'AAACGAAAGATTCGCT', 'AAACGAAAGCTCACTA', 'AAACGAAGTACTGACT', 'AAACGAAGTGTATCCA', 'AAACGAAGTTGCTCGG', 'AAACGAATCATTTGGG', 'AAACGAATCCGTATGA', 'AAACGAATCTCAACCC']
First 10 gene names: ['Xkr4', 'Gm19938', 'Sox17', 'Mrpl15', 'Lypla1', 'Tcea1', 'Rgs20', 'Atp6v1h', 'Npbwr1', '4732440D04Rik']

Layer Shapes in ldata
spliced: (6224, 29365)
unspliced: (6224, 29365)
ambiguous: (6224, 29365)
VelocityObject initialized successfully.
In [23]:
velocity_all = citeSEQ_all.getAdata()

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[23], line 1
----> 1 velocity_all = citeSEQ_all.getAdata()

NameError: name 'citeSEQ_all' is not defined
In [6]:
velocity_keratinocytes = citeSEQ_keratinocytes.getAdata()
velocity_keratinocytes.obsm["X_umap"] = velocity_keratinocytes.obsm["X_umap.harmony"].copy()
sc.pl.umap(velocity_keratinocytes, color="celltype", frameon=False,
           legend_loc='on data', title='', save='_celltypes_rpca.pdf')

WARNING: saving figure to file figures/umap_celltypes_rpca.pdf
No description has been provided for this image
In [9]:
scv.pl.proportions(velocity_keratinocytes, groupby="celltype")
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In [11]:
counts = velocity_keratinocytes.obs['celltype'].value_counts()

# Plot
plt.figure(figsize=(8, 4))
counts.plot(kind='bar')
plt.ylabel("Number of cells")
plt.xlabel("Cell type")
plt.title("Cell counts per cell type")
plt.xticks(rotation=45, ha='right')
plt.tight_layout()
plt.show()
No description has been provided for this image
In [ ]:
citeSEQ_keratinocytes.scVeloPreprocess()

Filtered out 19307 genes that are detected 20 counts (shared).
WARNING: Did not normalize X as it looks processed already. To enforce normalization, set `enforce=True`.
Normalized count data: spliced, unspliced.

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/preprocessing/utils.py:705: DeprecationWarning: `log1p` is deprecated since scVelo v0.3.0 and will be removed in a future version. Please use `log1p` from `scanpy.pp` instead.
  log1p(adata)
/Users/marissaesteban/Documents/GitHub/rnavelo-CITEseq/velocity scripts/VelocityObject.py:202: DeprecationWarning: Automatic neighbor calculation is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please compute neighbors first with Scanpy.
  scv.pp.moments(self.adata, n_pcs=30, n_neighbors=30)
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/preprocessing/moments.py:71: DeprecationWarning: `neighbors` is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please compute neighbors with Scanpy.
  neighbors(

Logarithmized X.
computing neighbors
    finished (0:00:09) --> added 
    'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
    finished (0:00:11) --> added 
    'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
In [15]:
citeSEQ_keratinocytes.computeVelocity()

recovering dynamics (using 1/16 cores)
WARNING: Unable to create progress bar. Consider installing `tqdm` as `pip install tqdm` and `ipywidgets` as `pip install ipywidgets`,
or disable the progress bar using `show_progress_bar=False`.
    finished (0:05:21) --> added 
    'fit_pars', fitted parameters for splicing dynamics (adata.var)
computing velocities
    finished (0:00:02) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/16 cores)
    finished (0:00:10) --> added 
    'velocity_graph', sparse matrix with cosine correlations (adata.uns)
In [17]:
velocity_keratinocytes = citeSEQ_keratinocytes.getAdata()
scv.pl.velocity_embedding_grid(
    velocity_keratinocytes,
    basis='X_umap',     
    color='celltype',
    dpi=150
)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [20]:
scv.pl.velocity_embedding_stream(
    velocity_keratinocytes,
    basis='X_umap',     
    color='celltype',
    dpi=150
)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [22]:
scv.pl.velocity(velocity_keratinocytes, ['Cdk1'], color='celltype')

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/numpy/core/fromnumeric.py:57: DeprecationWarning: Passing `np.nan` to mean no clipping in np.clip has always been unreliable, and is now deprecated. In future, this will always return nan, like it already does when min or max are arrays that contain nan. To skip a bound, pass either None or an np.inf of an appropriate sign.
  return bound(*args, **kwds)
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KERATINOCYTES SUBSET TO UNWOUNDED¶

In [18]:
keratinocytes_uw = citeSEQ_keratinocytes_uw.getAdata()
keratinocytes_uw.obsm["X_umap"] = keratinocytes_uw.obsm["X_umap_uw"].copy()
sc.pl.umap(keratinocytes_uw, color="celltype", frameon=False,
           legend_loc='on data', title='', save='_celltypes_rpca.pdf')

WARNING: saving figure to file figures/umap_celltypes_rpca.pdf
No description has been provided for this image
In [ ]:
citeSEQ_keratinocytes_uw.scVeloPreprocess()
citeSEQ_keratinocytes_uw.computeVelocity()

Filtered out 21202 genes that are detected 20 counts (shared).
WARNING: Did not normalize X as it looks processed already. To enforce normalization, set `enforce=True`.
Normalized count data: spliced, unspliced.
Logarithmized X.
computing neighbors

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/preprocessing/utils.py:705: DeprecationWarning: `log1p` is deprecated since scVelo v0.3.0 and will be removed in a future version. Please use `log1p` from `scanpy.pp` instead.
  log1p(adata)
/Users/marissaesteban/Documents/GitHub/rnavelo-CITEseq/velocity scripts/VelocityObject.py:203: DeprecationWarning: Automatic neighbor calculation is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please compute neighbors first with Scanpy.
  scv.pp.moments(self.adata, n_pcs=30, n_neighbors=30)
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/preprocessing/moments.py:71: DeprecationWarning: `neighbors` is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please compute neighbors with Scanpy.
  neighbors(

    finished (0:00:02) --> added 
    'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
    finished (0:00:03) --> added 
    'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
recovering dynamics (using 1/16 cores)
WARNING: Unable to create progress bar. Consider installing `tqdm` as `pip install tqdm` and `ipywidgets` as `pip install ipywidgets`,
or disable the progress bar using `show_progress_bar=False`.
    finished (0:02:00) --> added 
    'fit_pars', fitted parameters for splicing dynamics (adata.var)
computing velocities
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/16 cores)
    finished (0:00:02) --> added 
    'velocity_graph', sparse matrix with cosine correlations (adata.uns)
In [14]:
scv.pl.velocity_embedding_stream(
    keratinocytes_uw,
    basis='X_umap',     
    color='celltype',
    dpi=150
)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [13]:
keratinocytes_uw = citeSEQ_keratinocytes_uw.getAdata()
scv.pl.velocity_embedding_grid(
    keratinocytes_uw,
    basis='X_umap',     
    color='celltype',
    dpi=150
)

computing velocity embedding
    finished (0:00:00) --> added
    'velocity_umap', embedded velocity vectors (adata.obsm)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
using new embeddings¶

KERATINOCYTES SUBSET TO WOUNDED¶

In [16]:
keratinocytes_wo = citeSEQ_keratinocytes_wo.getAdata()
keratinocytes_wo.obsm["X_umap"] = keratinocytes_wo.obsm["X_umap_wo"].copy()
sc.pl.umap(keratinocytes_wo, color="celltype", frameon=False,
           legend_loc='on data', title='', save='_celltypes_rpca.pdf')

WARNING: saving figure to file figures/umap_celltypes_rpca.pdf
No description has been provided for this image
In [ ]:
citeSEQ_keratinocytes_wo.scVeloPreprocess()
citeSEQ_keratinocytes_wo.computeVelocity()

Filtered out 19990 genes that are detected 20 counts (shared).
WARNING: Did not normalize X as it looks processed already. To enforce normalization, set `enforce=True`.
Normalized count data: spliced, unspliced.
Logarithmized X.
computing neighbors

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/preprocessing/utils.py:705: DeprecationWarning: `log1p` is deprecated since scVelo v0.3.0 and will be removed in a future version. Please use `log1p` from `scanpy.pp` instead.
  log1p(adata)
/Users/marissaesteban/Documents/GitHub/rnavelo-CITEseq/velocity scripts/VelocityObject.py:203: DeprecationWarning: Automatic neighbor calculation is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please compute neighbors first with Scanpy.
  scv.pp.moments(self.adata, n_pcs=30, n_neighbors=30)
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/preprocessing/moments.py:71: DeprecationWarning: `neighbors` is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please compute neighbors with Scanpy.
  neighbors(

    finished (0:00:07) --> added 
    'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
    finished (0:00:07) --> added 
    'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
recovering dynamics (using 1/16 cores)
    finished (0:03:27) --> added 
    'fit_pars', fitted parameters for splicing dynamics (adata.var)
computing velocities
    finished (0:00:01) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/16 cores)
    finished (0:00:05) --> added 
    'velocity_graph', sparse matrix with cosine correlations (adata.uns)
In [20]:
scv.pl.velocity_embedding_stream(
    keratinocytes_wo,
    basis='X_umap',     
    color='celltype',
    dpi=150
)

computing velocity embedding
    finished (0:00:00) --> added
    'velocity_umap', embedded velocity vectors (adata.obsm)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [21]:
keratinocytes_wo = citeSEQ_keratinocytes_wo.getAdata()
scv.pl.velocity_embedding_grid(
    keratinocytes_wo,
    basis='X_umap',     
    color='celltype',
    dpi=150
)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image

More testing with adata objects¶

In [ ]:
keratinocytes_uw = citeSEQ_keratinocytes_uw.getAdata()
keratinocytes_wo = citeSEQ_keratinocytes_wo.getAdata()
In [38]:
scv.tl.rank_velocity_genes(keratinocytes_uw, groupby='celltype', min_corr=.3)
df = pd.DataFrame(keratinocytes_uw.uns['rank_velocity_genes']['names'])
df.head()

ranking velocity genes
    finished (0:00:00) --> added 
    'rank_velocity_genes', sorted scores by group ids (adata.uns) 
    'spearmans_score', spearmans correlation scores (adata.var)
Out[38]:
Ker.Cycling I Ker.Cycling II Ker.Cycling III IRS I IRS II Medulla Cortex Outer Bulge I Outer Bulge II Outer Bulge III ... Basal I Basal II Basal III Basal IV uHF I uHF II Spinous I Spinous II Spinous III Spinous IV
0 Plek2 Rp9 Krt80 Mgst1 Plek2 Jpt1 Rps11 Ptbp1 Oxct1 Serpinb5 ... Plek2 Ptgs1 Nedd4 Prdx2 Sf3b6 Sf3b6 Sar1b Sar1b Trib1 Uchl3
1 Reep5 Plek2 Gltp Cfl1 Hspb8 Bok Cstb Reep5 Atp2b4 Gng12 ... Tagln2 Prnp Pkib Elovl7 Uchl3 Bzw1 Cd44 Cd44 Tecr Ywhaq
2 Golim4 Ctsb Rnf11 Tuba4a Tpm4 Tagln2 Tagln2 Atp2b4 Wnt4 Jup ... Pkp1 Dstn Rcc2 Rpl35a Tkt Tkt Epcam Serpinb2 Snrpg Acat1
3 Notch1 Golim4 Npc2 Jpt1 Tagln2 Tpm4 Pof1b Oxct1 Ybx3 S100a11 ... Cstb Fst Rgcc Acat1 Mak16 Elovl4 Calm2 Hs3st1 Dusp7 Dstn
4 S100a11 Notch1 Notch1 Prkar1a Pkp1 Ralbp1 B2m Bbox1 Gng12 Mbd2 ... Hspb8 Sema3c Slc12a2 Anapc5 Bzw1 Hspe1 Ptp4a2 Epcam Mt2 Gnai1

5 rows × 22 columns

In [64]:
scv.tl.rank_velocity_genes(keratinocytes_wo, groupby='celltype', min_corr=.3)
df = pd.DataFrame(keratinocytes_wo.uns['rank_velocity_genes']['names'])
df.head()

ranking velocity genes

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/tools/utils.py:463: DeprecationWarning: Please import `rankdata` from the `scipy.stats` namespace; the `scipy.stats.stats` namespace is deprecated and will be removed in SciPy 2.0.0.
  from scipy.stats.stats import rankdata

    finished (0:00:10) --> added 
    'rank_velocity_genes', sorted scores by group ids (adata.uns) 
    'spearmans_score', spearmans correlation scores (adata.var)
Out[64]:
Ker.Cycling I Ker.Cycling II Ker.Cycling III IRS I IRS II Medulla Cortex Outer Bulge I Outer Bulge II Outer Bulge III ... Basal II Basal III Basal IV uHF I uHF II Spinous I Spinous II Spinous III Spinous IV Cornified
0 Anxa5 Mki67 Nedd4 Eif6 Tmem45a Tagln2 Acaa2 Actn1 Filip1l Pdzrn3 ... Efnb1 Nedd4 Macroh2a1 Uchl3 Uchl3 Ppp1r14c Serpinb2 Serpinb2 Sf3b6 Igfbp3
1 Fkbp1a Notch1 Notch1 Bok Acaa2 Anxa5 Ckmt1 Anxa8 Timp3 Lgals3 ... Hras Dsg1a Oxct1 Macroh2a1 Hopx Serpinb2 Mt1 Actr2 Anxa2 Serpinb2
2 Slc7a8 Lypd3 Cebpa Txndc17 Cux1 Plp2 Pkp1 Pdzrn3 Lgals3 Slc12a2 ... Trib1 Tob1 Hspb8 Vdr Adamts1 Actr2 Hif1a Hif1a Prkar1a Rps25
3 Tsc22d1 Golim4 Lima1 Efnb1 Gm49425 Wdr1 Psmb4 Smc6 Rnf217 Lsm4 ... Dsp Anapc5 Eef1g Anxa2 Itprid2 Itprid2 Sfr1 Hopx Sap18 Clca3a2
4 Golim4 Perp Vgll4 Rab11a Chmp2b Rai14 Lypd3 Rai14 Creb5 Actn1 ... Fst Macroh2a1 1810037I17Rik Sap18 Eif5 Il33 Ppp1r14c Hbegf Uchl3 Cyp51

5 rows × 23 columns

In [40]:
scv.pl.velocity(keratinocytes_uw, ['Plek2',  'Reep5', 'Golim4'], ncols=1, color='celltype')

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [41]:
scv.pl.velocity(keratinocytes_wo, ['Plek2',  'Reep5', 'Golim4'], ncols=1, color='celltype')

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/numpy/core/fromnumeric.py:57: DeprecationWarning: Passing `np.nan` to mean no clipping in np.clip has always been unreliable, and is now deprecated. In future, this will always return nan, like it already does when min or max are arrays that contain nan. To skip a bound, pass either None or an np.inf of an appropriate sign.
  return bound(*args, **kwds)
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [42]:
scv.tl.score_genes_cell_cycle(keratinocytes_wo)
scv.pl.scatter(keratinocytes_wo, color_gradients=['S_score', 'G2M_score'], smooth=True, perc=[5, 95])

calculating cell cycle phase
-->     'S_score' and 'G2M_score', scores of cell cycle phases (adata.obs)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [43]:
scv.tl.score_genes_cell_cycle(keratinocytes_uw)
scv.pl.scatter(keratinocytes_uw, color_gradients=['S_score', 'G2M_score'], smooth=True, perc=[5, 95])

calculating cell cycle phase
-->     'S_score' and 'G2M_score', scores of cell cycle phases (adata.obs)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [74]:
# stress genes: Fos, Jun Atf3, Egr1, IL1A
gene = 'Ptgs2'
if gene in keratinocytes_wo.var_names:
    scv.pl.velocity(
        keratinocytes_wo,
        var_names=[gene], 
        basis='umap',
        color='celltype'
    )
else:
    print("Gene not in adata")

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/numpy/core/fromnumeric.py:57: DeprecationWarning: Passing `np.nan` to mean no clipping in np.clip has always been unreliable, and is now deprecated. In future, this will always return nan, like it already does when min or max are arrays that contain nan. To skip a bound, pass either None or an np.inf of an appropriate sign.
  return bound(*args, **kwds)
No description has been provided for this image
In [75]:
# Proliferation genes: Mki67, Top2a, Cenpf, Pcna
gene = 'Top2a'
if gene in keratinocytes_uw.var_names:
    scv.pl.velocity(
        keratinocytes_uw,
        var_names=[gene], 
        basis='umap',
        color='celltype'
    )
else:
    print("Gene not in adata")

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/numpy/core/fromnumeric.py:57: DeprecationWarning: Passing `np.nan` to mean no clipping in np.clip has always been unreliable, and is now deprecated. In future, this will always return nan, like it already does when min or max are arrays that contain nan. To skip a bound, pass either None or an np.inf of an appropriate sign.
  return bound(*args, **kwds)
No description has been provided for this image

UN WOUNDED IFE¶

In [38]:
h5ad_path = "/Volumes/PortableSSD/SRSP/CITEseq_Keratinocytes/UW_IFE.h5ad"
loom_paths = ["/Volumes/PortableSSD/SRSP/CITEseq_looms/YS001/possorted_genome_bam_KLWV0.loom",
              "/Volumes/PortableSSD/SRSP/CITEseq_looms/YS002/possorted_genome_bam_PNEM4.loom",
              "/Volumes/PortableSSD/SRSP/CITEseq_looms/YS003/possorted_genome_bam_8Q2XV.loom",
              "/Volumes/PortableSSD/SRSP/CITEseq_looms/YS004/possorted_genome_bam_0XB2N.loom",
              "/Volumes/PortableSSD/SRSP/CITEseq_looms/YS005/possorted_genome_bam_HX08G.loom",
              "/Volumes/PortableSSD/SRSP/CITEseq_looms/YS006/possorted_genome_bam_751VB.loom"]

citeSEQ_Keratinocytes_IFE = VelocityObject(h5ad_path, loom_paths)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/utils.py:11: DeprecationWarning: The 'warn' function is deprecated, use 'warning' instead
  logging.warn(f"╭── " + message)
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/utils.py:12: DeprecationWarning: The 'warn' function is deprecated, use 'warning' instead
  logging.warn(f"╰──> at {frameinfo[2].filename}, line {frameinfo[2].lineno}")
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:biothings.client:Input sequence provided is already in string format. No operation performed
WARNING:biothings.client:Input sequence provided is already in string format. No operation performed
INFO:biothings.client:querying 1-248 ...

==== Converting ENSEMBL Genes ====
Total ldata genes: 33696
ENSEMBL-like genes: 248
Already-symbol-like genes: 33448 


INFO:biothings.client:Finished.
WARNING:biothings.client:13 input query terms found no hit:	['ENSMUSG00000095742', 'ENSMUSG00000095728', 'ENSMUSG00000095076', 'ENSMUSG00000121317', 'ENSMUSG000
INFO:biothings.client:Pass "returnall=True" to return complete lists of duplicate or missing query terms.

Mapped ENSMUSG → symbol: 203
Unmapped ENSMUSG: 45
Total ENSMUSG IDs after mapping:  45

=== Removing duplicates ===
adata
Cells (original): 3854
Genes (original): 30481
Duplicate cell barcodes: 0
Duplicate genes: 0
ldata
Cells (original): 45487
Genes (original): 33696
Duplicate cell barcodes: 235
Duplicate genes: 27

 adata after dedup: (3854, 30481)
ldata after dedup: (45252, 33696)

=== Subsetting cells by GENES and BARCODES ===
Overlapping Cells: 3794
Overlapping genes: 29365

adata shape: (3794, 29365)
ldata shape: (3794, 29365)
Cells match: True
Genes match: True

Layers in adata_subset: ['spliced', 'unspliced', 'ambiguous']
Spliced shape: (3794, 29365)
Unspliced shape: (3794, 29365)

=== Seurat-derived AnnData (adata) ===
Cells (obs): 3794
Genes (var): 29365
First 10 cell names: ['AAACGAAAGATTCGCT', 'AAACGAAAGCTCACTA', 'AAACGAAGTGTATCCA', 'AAACGAAGTTGCTCGG', 'AAACGAATCTCAACCC', 'AAACGCTCAAGAGATT', 'AAACGCTGTAGGTCAG', 'AAACGCTTCGCACTCT', 'AAAGAACCAACCGGAA', 'AAAGAACCATACAGAA']
First 10 gene names: ['Xkr4', 'Gm19938', 'Sox17', 'Mrpl15', 'Lypla1', 'Tcea1', 'Rgs20', 'Atp6v1h', 'Npbwr1', '4732440D04Rik']

=== Loom Spliced/Unspliced Data (ldata) ===
Cells (obs): 3794
Genes (var): 29365
First 10 cell names: ['AAACGAAAGATTCGCT', 'AAACGAAAGCTCACTA', 'AAACGAAGTGTATCCA', 'AAACGAAGTTGCTCGG', 'AAACGAATCTCAACCC', 'AAACGCTCAAGAGATT', 'AAACGCTGTAGGTCAG', 'AAACGCTTCGCACTCT', 'AAAGAACCAACCGGAA', 'AAAGAACCATACAGAA']
First 10 gene names: ['Xkr4', 'Gm19938', 'Sox17', 'Mrpl15', 'Lypla1', 'Tcea1', 'Rgs20', 'Atp6v1h', 'Npbwr1', '4732440D04Rik']

Layer Shapes in ldata
spliced: (3794, 29365)
unspliced: (3794, 29365)
ambiguous: (3794, 29365)
VelocityObject initialized successfully.
In [39]:
velocity_ker_ife = citeSEQ_Keratinocytes_IFE.getAdata()
scv.pl.proportions(velocity_ker_ife, groupby="celltype")
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In [54]:
# pre process and compute velocity

citeSEQ_Keratinocytes_IFE.scVeloPreprocess(n_pcs=20)
citeSEQ_Keratinocytes_IFE.computeVelocity()

Filtered out 73 genes that are detected 20 counts (spliced).
WARNING: Did not normalize X as it looks processed already. To enforce normalization, set `enforce=True`.
WARNING: Did not normalize spliced as it looks processed already. To enforce normalization, set `enforce=True`.
WARNING: Did not normalize unspliced as it looks processed already. To enforce normalization, set `enforce=True`.
WARNING: adata.X seems to be already log-transformed.
Logarithmized X.
computing moments based on connectivities

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/preprocessing/utils.py:705: DeprecationWarning: `log1p` is deprecated since scVelo v0.3.0 and will be removed in a future version. Please use `log1p` from `scanpy.pp` instead.
  log1p(adata)

    finished (0:00:02) --> added 
    'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
recovering dynamics (using 1/16 cores)
    finished (0:00:52) --> added 
    'fit_pars', fitted parameters for splicing dynamics (adata.var)
computing velocities
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/16 cores)
    finished (0:00:01) --> added 
    'velocity_graph', sparse matrix with cosine correlations (adata.uns)
In [55]:
velocity_ker_ife.obsm["X_umap"] = velocity_ker_ife.obsm["X_umap.harmony"].copy()
scv.pl.velocity_embedding_stream(
    velocity_ker_ife,
    basis='X_umap',     
    color='celltype',
    palette="tab20",
    dpi=150
)

computing velocity embedding
    finished (0:00:00) --> added
    'velocity_umap', embedded velocity vectors (adata.obsm)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
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In [56]:
scv.pl.velocity_embedding_grid(
    velocity_ker_ife,
    basis='X_umap',     
    color='celltype',
    palette="tab20",
    dpi=150
)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
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In [47]:
scv.tl.rank_velocity_genes(velocity_ker_ife, groupby='celltype', min_corr=.3)
df = pd.DataFrame(velocity_ker_ife.uns['rank_velocity_genes']['names'])
df.head(8)

ranking velocity genes
    finished (0:00:00) --> added 
    'rank_velocity_genes', sorted scores by group ids (adata.uns) 
    'spearmans_score', spearmans correlation scores (adata.var)
Out[47]:
Ker.Cycling I Ker.Cycling II Ker.Cycling III Basal II Basal III Basal IV Spinous I Spinous II Spinous III Spinous IV
0 Plek2 Plek2 Krt80 Ptgs1 Smagp Lgals3 Sar1b Ifi202b Mt2 Ywhaq
1 S100a11 Mki67 Pkp1 Prnp H2bc4 Ywhaq Prmt1 Arhgdib H2aj Uchl3
2 Dpy30 Sdc1 H2bc4 Sema3c Nedd4 Nudc Dek Sar1b Lrrc59 Nudc
3 Pkp1 Tagln2 Nr4a1 Cct6a Pkib Lmo4 Ptp4a2 Sprr1b Tecr Lgals3
4 Tmprss4 Rp9 Maff Atp2b1 Tuba1b Pkib Igfbp3 Il33 Ak2 Tkt
5 Col17a1 Pkp1 Slc12a2 Itgb1 Ldha Oxct1 Hspd1 Cd44 Rsl1d1 Sugt1
6 Csrp1 Cnih4 Bcl11b Rexo2 Rcc2 Hoxa7 Uchl3 Uchl3 Rabac1 Acat1
7 Bcl11b S100a11 Atp2b4 Cxcl14 Slc12a2 Smagp Il33 Serpinb2 Atf3 Hagh
In [48]:
import scanpy as sc

gene = "Krt14"  # change me
genes = ["Krt14", "Krt1", "Cdk1", "Trp63", "Fos", "Cdkn1a"]

sc.pl.embedding(
    velocity_ker_ife,
    basis="umap",
    color=genes,
    ncols=3   # 3 columns × 2 rows
)
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In [51]:
scv.pl.velocity(velocity_ker_ife, ['Smagp',  'H2bc4', 'Nedd4'], ncols=1, color='celltype')

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
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